Seed removal behaviors of rodents are largely influenced by microhabitat. Although the karst ecosystem is composed of a broad variety of microhabitats, we have no information on how they affect such behaviors. We investigated rodents’ seed removal behaviors in four karst microhabitats (stone cavern, stone groove, stone surface, and soil surface) using three types of Kmeria septentrionalis seeds: fresh, black (intact seeds with black aril that dehydrates and darkens), and exposed (clean seeds without the aril). We show that Rattus norvegicus, Leopoldamys edwardsi and Rattus flavipectus were the predominant seed predators. Even though all seed types experienced a high removal rate in all four microhabitats, but rodents preferentially removed seeds from the three stone microhabitats (stone caves: 69.71 ± 2.74%; stone surface: 60.53 ± 2.90%; stone groove: 56.94 ± 2.91%) compared to the soil surface (53.90 ± 2.92%). Seeds that had been altered by being exposed to the environment were more attractive to rodents than fresh seeds (76.25 ± 2.20% versus 36.18 ± 2.29%). The seed removal behavior of rodents was significantly affected by the microhabitat and seed type. Finally, seeds that had fallen on the soil surface microhabitat incurred a lower predation risk than seeds fallen on other microhabitats, which increased their probability to germinate. Our results indicate that the lower predation rate of seeds from the endangered K. septentrionalis dropped on the soil surface increases trees’ likelihood of survival.

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